1) Search the module system for any application(s) that you need for your research.
For my research, I use a molecular dynamics tool called gromacs:
$ module list
Currently Loaded Modules:
1) intel/16.0.1 2) cray_mpich/7.3.0 3) TACC/1.0
$ module spider gromacs
---------------------------------------------------------------------------------------------------------
gromacs:
---------------------------------------------------------------------------------------------------------
Description:
molecular dynamics simulation package
Versions:
gromacs/5.0.6
gromacs/5.1.2
2) Figure out if any dependencies are required to load the module.
$ module spider gromacs/5.1.2 # carefully read output
...
You will need to load all module(s) on any one of the lines below before the "gromacs/5.1.2" module is av
ailable to load.
intel/16.0.1 cray_mpich/7.3.0
...
It looks like I must have intel/16.0.1 and cray_mpich/7.3.0 loaded in order to load gromacs/5.1.2. I already have those loaded, so I should be ready to go.
3) Load the module and determine what effect it has on your environment.
$ module show gromacs/5.1.2 # carefully read output
...
prepend_path("PATH","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/bin")
prepend_path("LD_LIBRARY_PATH","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/lib64")
setenv("TACC_GROMACS_DIR","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2")
setenv("TACC_GROMACS_INC","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/include")
setenv("TACC_GROMACS_LIB","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/lib64")
setenv("TACC_GROMACS_BIN","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/bin")
setenv("TACC_GROMACS_DOC","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share")
setenv("GMXLIB","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/gromacs/top")
append_path("MANPATH","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/share/man")
append_path("PKG_CONFIG_PATH","/opt/apps/intel16/cray_mpich_7_3/gromacs/5.1.2/lib/pkgconfig")
...
It looks like the major changes are to prepend the PATH and LD_LIBRARY_PATH environment variables, and to define several new variables with _GROMACS_ in the name (plus a few other minor changes).
$ echo $PATH
$ echo $TACC_GROMACS_DIR
$ module load gromacs/5.1.2
$ module list
$ echo $PATH
$ echo $TACC_GROMACS_DIR
4) Make sure the desired executables (and correct version) are in your PATH.
$ which gmx
# gmx --version # do not run these applications on the login node, but checking the version is okay